Characterization of Genetic Variability of Venezuelan Equine Encephalitis Viruses.
Venezuelan equine encephalitis virus (VEEV) is a mosquito-borne alphavirus that has caused large outbreaks of severe illness in both horses and humans. New approaches are needed to rapidly infer the origin of a newly discovered VEEV strain, estimate its equine amplification and resultant epidemic po...
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doaj-1faf05b8ed1b46c9a499593a34ae55b52020-11-25T00:40:18ZengPublic Library of Science (PLoS)PLoS ONE1932-62032016-01-01114e015260410.1371/journal.pone.0152604Characterization of Genetic Variability of Venezuelan Equine Encephalitis Viruses.Shea N GardnerKevin McLoughlinNicholas A BeJonathan AllenScott C WeaverNaomi ForresterMathilde GuerboisCrystal JaingVenezuelan equine encephalitis virus (VEEV) is a mosquito-borne alphavirus that has caused large outbreaks of severe illness in both horses and humans. New approaches are needed to rapidly infer the origin of a newly discovered VEEV strain, estimate its equine amplification and resultant epidemic potential, and predict human virulence phenotype. We performed whole genome single nucleotide polymorphism (SNP) analysis of all available VEE antigenic complex genomes, verified that a SNP-based phylogeny accurately captured the features of a phylogenetic tree based on multiple sequence alignment, and developed a high resolution genome-wide SNP microarray. We used the microarray to analyze a broad panel of VEEV isolates, found excellent concordance between array- and sequence-based SNP calls, genotyped unsequenced isolates, and placed them on a phylogeny with sequenced genomes. The microarray successfully genotyped VEEV directly from tissue samples of an infected mouse, bypassing the need for viral isolation, culture and genomic sequencing. Finally, we identified genomic variants associated with serotypes and host species, revealing a complex relationship between genotype and phenotype.http://europepmc.org/articles/PMC4824352?pdf=render |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Shea N Gardner Kevin McLoughlin Nicholas A Be Jonathan Allen Scott C Weaver Naomi Forrester Mathilde Guerbois Crystal Jaing |
spellingShingle |
Shea N Gardner Kevin McLoughlin Nicholas A Be Jonathan Allen Scott C Weaver Naomi Forrester Mathilde Guerbois Crystal Jaing Characterization of Genetic Variability of Venezuelan Equine Encephalitis Viruses. PLoS ONE |
author_facet |
Shea N Gardner Kevin McLoughlin Nicholas A Be Jonathan Allen Scott C Weaver Naomi Forrester Mathilde Guerbois Crystal Jaing |
author_sort |
Shea N Gardner |
title |
Characterization of Genetic Variability of Venezuelan Equine Encephalitis Viruses. |
title_short |
Characterization of Genetic Variability of Venezuelan Equine Encephalitis Viruses. |
title_full |
Characterization of Genetic Variability of Venezuelan Equine Encephalitis Viruses. |
title_fullStr |
Characterization of Genetic Variability of Venezuelan Equine Encephalitis Viruses. |
title_full_unstemmed |
Characterization of Genetic Variability of Venezuelan Equine Encephalitis Viruses. |
title_sort |
characterization of genetic variability of venezuelan equine encephalitis viruses. |
publisher |
Public Library of Science (PLoS) |
series |
PLoS ONE |
issn |
1932-6203 |
publishDate |
2016-01-01 |
description |
Venezuelan equine encephalitis virus (VEEV) is a mosquito-borne alphavirus that has caused large outbreaks of severe illness in both horses and humans. New approaches are needed to rapidly infer the origin of a newly discovered VEEV strain, estimate its equine amplification and resultant epidemic potential, and predict human virulence phenotype. We performed whole genome single nucleotide polymorphism (SNP) analysis of all available VEE antigenic complex genomes, verified that a SNP-based phylogeny accurately captured the features of a phylogenetic tree based on multiple sequence alignment, and developed a high resolution genome-wide SNP microarray. We used the microarray to analyze a broad panel of VEEV isolates, found excellent concordance between array- and sequence-based SNP calls, genotyped unsequenced isolates, and placed them on a phylogeny with sequenced genomes. The microarray successfully genotyped VEEV directly from tissue samples of an infected mouse, bypassing the need for viral isolation, culture and genomic sequencing. Finally, we identified genomic variants associated with serotypes and host species, revealing a complex relationship between genotype and phenotype. |
url |
http://europepmc.org/articles/PMC4824352?pdf=render |
work_keys_str_mv |
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